95 Yamaha warrior Should my motor spin freely i just rebuilt the motor and the counter..

[kotton0405]

...balance hits the rod? i lined it up like it shows to do in the manual

 

[santa is dead]

nothing should be hitting anything,time to do it over again.

 

[Dan W]

Take it apart and do it again, look for the pieces that are knocking.
I'd bet you have the wrong,longer bolt in it.
If yiou hear it while turning by hand what about under powere at 1K -8K RPM?